When comparing towers to bookshelves, do you let a subwoofer into the mix?

I'm presently comparing bookshelves to towers in my listening space.
Until today, I've just compared the speakers without adding my sub.
But since I would be using a sub (especially with bookshelves) it seems fair to add that in.

How would you make a final judgment comparing two speakers?

Naked (no subs) -- Speaker A vs. Speaker B?
or
With Sub (since that's how things would actually happen)?

Perhaps this question answers itself with "both" but I'm curious what folks do in this situation. It seems unfair to blame the bookshelf for not having the low end of the tower, but I would be using it with a sub, so that would allow me to judge on just the non-bass performance